RPE_ORYSJ
ID RPE_ORYSJ Reviewed; 274 AA.
AC Q9ZTP5; Q10R77; Q8S7V5;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 2.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Ribulose-phosphate 3-epimerase, chloroplastic;
DE EC=5.1.3.1 {ECO:0000250|UniProtKB:Q43157};
DE AltName: Full=Pentose-5-phosphate 3-epimerase;
DE Short=PPE;
DE AltName: Full=R5P3E;
DE Short=RPE;
DE Flags: Precursor;
GN Name=RPE; Synonyms=RPE2; OrderedLocusNames=Os03g0169100, LOC_Os03g07300;
GN ORFNames=OsJ_09567 {ECO:0000312|EMBL:EEE58398.1}, OSJNBa0091P11.10;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=9843485; DOI=10.1093/emboj/17.23.6799;
RA Favery B., Lecomte P., Gil N., Bechtold N., Bouchez D., Dalmasso A.,
RA Abad P.;
RT "RPE, a plant gene involved in early developmental steps of nematode
RT feeding cells.";
RL EMBO J. 17:6799-6811(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP PROTEIN SEQUENCE [LARGE SCALE ANALYSIS] OF 40-46, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC STRAIN=cv. Nipponbare;
RX PubMed=16758443; DOI=10.1002/pmic.200600043;
RA Nozu Y., Tsugita A., Kamijo K.;
RT "Proteomic analysis of rice leaf, stem and root tissues during growth
RT course.";
RL Proteomics 6:3665-3670(2006).
CC -!- FUNCTION: Catalyzes the reversible epimerization of D-ribulose 5-
CC phosphate to D-xylulose 5-phosphate. {ECO:0000250|UniProtKB:Q43157}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
CC Xref=Rhea:RHEA:13677, ChEBI:CHEBI:57737, ChEBI:CHEBI:58121;
CC EC=5.1.3.1; Evidence={ECO:0000250|UniProtKB:Q43157};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Note=Binds 1 divalent metal cation per subunit. Active with Co(2+),
CC Fe(2+), Mn(2+) and Zn(2+). {ECO:0000250|UniProtKB:Q96AT9};
CC -!- PATHWAY: Carbohydrate biosynthesis; Calvin cycle.
CC {ECO:0000250|UniProtKB:Q43157}.
CC -!- SUBUNIT: Homooctamer. {ECO:0000250|UniProtKB:Q43157}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000250|UniProtKB:Q43157}.
CC -!- SIMILARITY: Belongs to the ribulose-phosphate 3-epimerase family.
CC {ECO:0000305}.
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DR EMBL; AF047444; AAD09955.1; -; mRNA.
DR EMBL; AC073556; AAL84303.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF94188.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11010.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS82507.1; -; Genomic_DNA.
DR EMBL; CM000140; EEE58398.1; -; Genomic_DNA.
DR EMBL; AK061772; BAG88103.1; -; mRNA.
DR EMBL; AK066306; BAG89902.1; -; mRNA.
DR EMBL; AK099215; BAG94000.1; -; mRNA.
DR RefSeq; XP_015630737.1; XM_015775251.1.
DR AlphaFoldDB; Q9ZTP5; -.
DR SMR; Q9ZTP5; -.
DR STRING; 4530.OS03T0169100-01; -.
DR PaxDb; Q9ZTP5; -.
DR PRIDE; Q9ZTP5; -.
DR EnsemblPlants; Os03t0169100-01; Os03t0169100-01; Os03g0169100.
DR GeneID; 4331761; -.
DR Gramene; Os03t0169100-01; Os03t0169100-01; Os03g0169100.
DR KEGG; osa:4331761; -.
DR eggNOG; KOG3111; Eukaryota.
DR HOGENOM; CLU_054856_1_1_1; -.
DR InParanoid; Q9ZTP5; -.
DR OMA; CDLILIM; -.
DR OrthoDB; 1554029at2759; -.
DR PlantReactome; R-OSA-1119519; Calvin cycle.
DR UniPathway; UPA00116; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q9ZTP5; OS.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0010319; C:stromule; IEA:EnsemblPlants.
DR GO; GO:0004750; F:D-ribulose-phosphate 3-epimerase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IBA:GO_Central.
DR GO; GO:0044262; P:cellular carbohydrate metabolic process; IBA:GO_Central.
DR GO; GO:0009052; P:pentose-phosphate shunt, non-oxidative branch; IBA:GO_Central.
DR GO; GO:0019253; P:reductive pentose-phosphate cycle; IEA:UniProtKB-UniPathway.
DR GO; GO:0009409; P:response to cold; IEA:EnsemblPlants.
DR GO; GO:0009624; P:response to nematode; IEA:EnsemblPlants.
DR CDD; cd00429; RPE; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02227; RPE; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR026019; Ribul_P_3_epim.
DR InterPro; IPR000056; Ribul_P_3_epim-like.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR11749; PTHR11749; 1.
DR Pfam; PF00834; Ribul_P_3_epim; 1.
DR PIRSF; PIRSF001461; RPE; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR01163; rpe; 1.
DR PROSITE; PS01085; RIBUL_P_3_EPIMER_1; 1.
DR PROSITE; PS01086; RIBUL_P_3_EPIMER_2; 1.
PE 1: Evidence at protein level;
KW Calvin cycle; Carbohydrate metabolism; Chloroplast; Cobalt;
KW Direct protein sequencing; Iron; Isomerase; Manganese; Membrane;
KW Metal-binding; Pentose shunt; Plastid; Reference proteome; Thylakoid;
KW Transit peptide; Zinc.
FT TRANSIT 1..39
FT /note="Chloroplast"
FT /evidence="ECO:0000269|PubMed:16758443"
FT CHAIN 40..274
FT /note="Ribulose-phosphate 3-epimerase, chloroplastic"
FT /id="PRO_0000025415"
FT ACT_SITE 83
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT ACT_SITE 225
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 56
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 81
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 83
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 114
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 192..195
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 225..227
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 225
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 247..248
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT CONFLICT 211..213
FT /note="RLC -> KYV (in Ref. 1; AAD09955)"
FT /evidence="ECO:0000305"
FT CONFLICT 267..268
FT /note="QK -> KR (in Ref. 1; AAD09955)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 274 AA; 29035 MW; FB3C2BE2289E93CD CRC64;
MASPSSSSSL CSTFASPRAA SLGRRLAFSS PRKAFRVRAS SRVDKFSKND IIVSPSILSA
NFSKLGEQVK AVEVAGCDWI HVDVMDGRFV PNITIGPLVV DALRPVTDLP LDVHLMIVEP
EQRVPDFIKA GADIVSVHCE QSSTIHLHRT VNQIKSLGAK AGVVLNPATP LTAIDYVLDV
VDLVLIMSVN PGFGGQSFIE SQVKKIAELR RLCAEKGVNP WIEVDGGVGP KNAYKVIEAG
ANAIVAGSAV FGAPDYAEAI KGIKTSQKPV AVPA
